Opened 4 years ago

Closed 4 years ago

#6313 closed defect (fixed)

atom_search_lib missing

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC)
Description
AddH seems broken in the daily build.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde demo crystal_intro

> set selectionWidth 4

Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description | UniProt  
A | predicted microcompartment protein | A5N734_CLOK5  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1 to IUPAC-IUB
standards.  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description | UniProt  
1.2/A | predicted microcompartment protein | A5N734_CLOK5  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.303, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0575,0.0575, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.603, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.366, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
ISOLDE: started sim  

> select clear

> graphics rate true

> ui tool show Shell

> graphics rate false

QCoreApplication::exec: The event loop is already running  

ISOLDE: paused sim  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  

> select clear

> graphics rate true

> graphics rate false

QCoreApplication::exec: The event loop is already running  

[Repeated 1 time(s)]Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  
ISOLDE: started sim  

> select clear

> st

[Repeated 52 time(s)]Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #1

Deleting Crystallographic maps (3io0-sf.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> open 2rf4 structureFactors true overSampling 2

Summary of feedback from opening 2rf4 fetched from pdb  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
No free flags detected in this dataset! Automatically generated a new random
set with 874 free from 18174 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 3.099903641564608  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 34,34,34, pixel
0.766,0.761,0.727, shown at level 0.191, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 34,34,34, pixel
0.766,0.761,0.727, shown at level -0.0889,0.0889, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 34,34,34, pixel
0.766,0.761,0.727, shown at level 0.412, step 1, values float32  
2rf4 title:  
Crystal structure of the RNA Polymerase I subcomplex A14/43 [more info...]  
  
Chain information for 2rf4  
---  
Chain | Description | UniProt  
1.2/A 1.2/C 1.2/E | DNA-directed RNA polymerase I subunit RPA4 | RPA43_YEAST  
1.2/B 1.2/D 1.2/F | DNA-directed RNA polymerase I subunit RPA4 | RPA14_YEAST  
  
2rf4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 41 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 34,34,34, pixel
0.766,0.761,0.727, shown at level 0.205, step 1, values float32  

> alphafold match #1

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
Fetching compressed AlphaFold P46669 from
https://alphafold.ebi.ac.uk/files/AF-P46669-F1-model_v2.cif  
Fetching compressed AlphaFold P50106 from
https://alphafold.ebi.ac.uk/files/AF-P50106-F1-model_v2.cif  
2 AlphaFold models found using UniProt identifiers: P46669 (chains
A,A,C,C,E,E), P50106 (chains B,B,D,D,F,F)  
AlphaFold chains matching 2rf4  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
B | RPA14_YEAST | P50106 | 1.71 | 52 | 61 | 100  
B | RPA14_YEAST | P50106 | 1.57 | 35 | 61 | 100  
D | RPA14_YEAST | P50106 | 1.59 | 52 | 60 | 100  
D F | RPA14_YEAST | P50106 | 1.65 | 35 | 60 | 100  
F | RPA14_YEAST | P50106 | 1.69 | 52 | 60 | 100  
A | RPA43_YEAST | P46669 | 1.66 | 171 | 174 | 100  
A | RPA43_YEAST | P46669 | 3.00 | 42 | 174 | 100  
C | RPA43_YEAST | P46669 | 1.48 | 171 | 172 | 100  
C | RPA43_YEAST | P46669 | 3.25 | 42 | 172 | 100  
E | RPA43_YEAST | P46669 | 1.58 | 171 | 175 | 100  
E | RPA43_YEAST | P46669 | 3.75 | 42 | 175 | 100  
  
Opened 12 AlphaFold models  

> show #2

> select /A,B

4213 atoms, 4302 bonds, 2 pseudobonds, 535 residues, 6 models selected  

> close #1.3#1-2#1.1-2

Deleting Crystallographic maps (2rf4-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_32  
Deleting (LIVE) MDFF potential  

> open 3brw structureFactors true

Summary of feedback from opening 3brw fetched from pdb  
---  
warnings | Unknown polymer entity '5' near line 10839  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Fetching compressed mmCIF 3brw from
http://files.rcsb.org/download/3brw.cif  
Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif  
Fetching compressed 3brw structure factors from
http://files.rcsb.org/download/3brw-sf.cif  
Resolution: 3.400053747470817  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,28,22, pixel 1.09,1.09,1.13,
shown at level 0.155, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,28,22, pixel 1.09,1.09,1.13,
shown at level -0.0584,0.0584, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_40 as #1.1.1.4, grid size 38,28,22, pixel
1.09,1.09,1.13, shown at level 0.332, step 1, values float32  
3brw title:  
Structure of the Rap-RapGAP complex [more info...]  
  
Chain information for 3brw  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C | Rap1 GTPase-activating protein 1 | RPGP1_HUMAN  
1.2/D | Ras-related protein Rap-1b | RAP1B_HUMAN  
  
Non-standard residues in 3brw #1.2  
---  
BEF — beryllium trifluoride ion  
MG — magnesium ion  
  
3brw mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 133 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,28,22, pixel
1.09,1.09,1.13, shown at level 0.152, step 1, values float32  

> alphafold match #1

Fetching compressed AlphaFold P47736 from
https://alphafold.ebi.ac.uk/files/AF-P47736-F1-model_v2.cif  
Fetching compressed AlphaFold P61224 from
https://alphafold.ebi.ac.uk/files/AF-P61224-F1-model_v2.cif  
2 AlphaFold models found using UniProt identifiers: P47736 (chains A,B,C),
P61224 (chain D)  
AlphaFold chains matching 3brw  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
D | RAP1B_HUMAN | P61224 | 0.83 | 167 | 167 | 100  
A | RPGP1_HUMAN | P47736 | 1.85 | 341 | 336 | 99  
B | RPGP1_HUMAN | P47736 | 1.27 | 341 | 337 | 99  
C | RPGP1_HUMAN | P47736 | 1.80 | 341 | 332 | 99  
  
Opened 4 AlphaFold models  

> show #2

> isolde restrain distances #1/A templateAtoms #2/A adjustForConfidence true
> displayThreshold 0.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in
model #2.1 to IUPAC-IUB standards.  
Fetching compressed Alphafold P47736 PAE from
https://alphafold.ebi.ac.uk/files/AF-P47736-F1-predicted_aligned_error_v1.json  
RMSD between 330 pruned atom pairs is 1.430 angstroms; (across all 336 pairs:
1.835)  
RMSD between 5 pruned atom pairs is 2.688 angstroms; (across all 6 pairs:
3.841)  

> isolde restrain distances #1/B templateAtoms #2/B adjustForConfidence true
> displayThreshold 0.5

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in
model #2.2 to IUPAC-IUB standards.  
RMSD between 334 pruned atom pairs is 1.071 angstroms; (across all 337 pairs:
1.249)  

> select #1/A,B

5418 atoms, 5551 bonds, 676 residues, 1 model selected  

> hide #!2 models

> select clear

> show #!2 models

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 3brw #1.2/A THR 76 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 3brw #1.2/A LEU 411 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to 3brw #1.2/B LYS 78 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 3brw #1.2/C LYS 78 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 3brw #1.2/C LEU 411 CB because it is missing heavy-
atom bond partners  
notes | Termini for 3brw (#1.2) chain A determined from SEQRES records  
Termini for 3brw (#1.2) chain B determined from SEQRES records  
Termini for 3brw (#1.2) chain C determined from SEQRES records  
Termini for 3brw (#1.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: 3brw #1.2/D MET 1  
Chain-initial residues that are not actual N termini: 3brw #1.2/A THR 76, 3brw
#1.2/B LYS 78, 3brw #1.2/C LYS 78, 3brw #1.2/C PRO 330  
Chain-final residues that are actual C termini: 3brw #1.2/D ARG 167  
Chain-final residues that are not actual C termini: 3brw #1.2/A LEU 411, 3brw
#1.2/B ASP 414, 3brw #1.2/C GLY 325, 3brw #1.2/C GLY 413  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 302, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 161, in hbond_add_hydrogens  
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 168, in hbond_add_hydrogens  
_make_shared_data(session, structures, in_isolation)  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\addh\cmd.py", line 365, in _make_shared_data  
from chimerax.atom_search import AtomSearchTree  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\atom_search\\__init__.py", line 15, in <module>  
import chimerax.atom_search_lib  
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'  
  
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'  
  
File "C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\chimerax\atom_search\\__init__.py", line 15, in  
import chimerax.atom_search_lib  
  
See log for complete Python traceback.  
  

> ui tool show Shell

C:\Program Files\ChimeraX-daily\bin\lib\site-
packages\jedi\inference\compiled\subprocess\functions.py:22: UserWarning:
Module chimerax.atom_search.ast not importable in path
['C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\1.4\\\site-
packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\python39.zip',
'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\DLLs', 'C:\\\Program
Files\\\ChimeraX-daily\\\bin\\\lib', 'C:\\\Program Files\\\ChimeraX-
daily\\\bin', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
packages\\\win32', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
packages\\\win32\\\lib', 'C:\\\Program Files\\\ChimeraX-
daily\\\bin\\\lib\\\site-packages\\\Pythonwin', '.', 'C:\\\Program
Files\\\ChimeraX-daily\\\bin\\\lib\\\site-packages\\\IPython\\\extensions'].  
return access.load_module(inference_state, **kwargs)  




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_GB.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203030220
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4.dev0
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.2
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Already fixed, I see. Rebuilt atom_search? from the current source and it works again. :)
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 04 March 2022 12:19
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #6313: ChimeraX bug report submission

#6313: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Windows-10-10.0.19041
 ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC)
 Description
 AddH seems broken in the daily build.

 Log:
 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color {arguments} bychain; color {arguments} byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)
 © 2016-2022 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > isolde demo crystal_intro

 > set selectionWidth 4

 Cached rama8000-cispro data not found. Regenerating from text file. This
 is
 normal if running ISOLDE for the first time
 Cached rama8000-transpro data not found. Regenerating from text file. This
 is
 normal if running ISOLDE for the first time
 Cached rama8000-gly-sym data not found. Regenerating from text file. This
 is
 normal if running ISOLDE for the first time
 Cached rama8000-prepro-noGP data not found. Regenerating from text file.
 This
 is normal if running ISOLDE for the first time
 Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
 This is normal if running ISOLDE for the first time
 Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
 file. This is normal if running ISOLDE for the first time
 before.pdb title:
 Crystal structure of etub from clostridium kluyveri [more info...]

 Chain information for before.pdb #1
 ---
 Chain | Description | UniProt
 A | predicted microcompartment protein | A5N734_CLOK5

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 12 residues in model #1 to IUPAC-
 IUB
 standards.
 before.pdb title:
 Crystal structure of etub from clostridium kluyveri [more info...]

 Chain information for before.pdb
 ---
 Chain | Description | UniProt
 1.2/A | predicted microcompartment protein | A5N734_CLOK5

 Cached rota8000-val data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-leu data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-ile data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-pro data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-phe data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-tyr data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-trp data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-ser data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-thr data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-cys data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-met data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-lys data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-his data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-arg data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-asp data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-asn data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-gln data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time
 Cached rota8000-glu data not found. Regenerating from text file. This is
 normal if running ISOLDE for the first time

 WARNING: multiple experimental reflection datasets found:
 (dataset) FOBS, SIGFOBS,
 (dataset) IOBS, SIGIOBS,
 (dataset) DANO, SIGDANO,
 (dataset) F(+), SIGF(+), F(-), SIGF(-),
 (dataset) I(+), SIGI(+), I(-), SIGI(-)
 Automatically choosing "(dataset) FOBS, SIGFOBS".

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown
 at
 level 0.303, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown
 at
 level -0.0575,0.0575, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel
 0.723,
 shown at level 0.603, step 1, values float32
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
 shown at level 0.366, step 1, values float32
 Loaded crystallographic demo: PDB ID 3io0
 Forcefield cache not found or out of date. Regenerating from ffXML files.
 This
 is normal if running ISOLDE for the first time, or after upgrading OpenMM.
 Done loading forcefield
 ISOLDE: started sim

 > select clear

 > graphics rate true

 > ui tool show Shell

 > graphics rate false

 QCoreApplication::exec: The event loop is already running

 ISOLDE: paused sim
 Updating bulk solvent parameters...
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim
 ISOLDE: started sim

 > select clear

 > graphics rate true

 > graphics rate false

 QCoreApplication::exec: The event loop is already running

 [Repeated 1 time(s)]Updating bulk solvent parameters...
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > select #1

 3348 atoms, 3371 bonds, 229 residues, 30 models selected
 ISOLDE: started sim

 > select clear

 > st

 [Repeated 52 time(s)]Updating bulk solvent parameters...
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > close #1

 Deleting Crystallographic maps (3io0-sf.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_sharp_29
 Deleting (LIVE) MDFF potential

 > open 2rf4 structureFactors true overSampling 2

 Summary of feedback from opening 2rf4 fetched from pdb
 ---
 warnings | WARNING: multiple experimental reflection datasets found:
 F_meas_au, F_meas_sigma_au,
 pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,
 pdbx_anom_difference, pdbx_anom_difference_sigma
 Automatically choosing "F_meas_au, F_meas_sigma_au".
 No free flags detected in this dataset! Automatically generated a new
 random
 set with 874 free from 18174 observed reflections. You should save your
 data
 to a new MTZ file and use this for any future rebuilding/refinement.
 notes | Resolution: 3.099903641564608

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 34,34,34, pixel
 0.766,0.761,0.727, shown at level 0.191, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 34,34,34, pixel
 0.766,0.761,0.727, shown at level -0.0889,0.0889, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 34,34,34, pixel
 0.766,0.761,0.727, shown at level 0.412, step 1, values float32
 2rf4 title:
 Crystal structure of the RNA Polymerase I subcomplex A14/43 [more info...]

 Chain information for 2rf4
 ---
 Chain | Description | UniProt
 1.2/A 1.2/C 1.2/E | DNA-directed RNA polymerase I subunit RPA4 |
 RPA43_YEAST
 1.2/B 1.2/D 1.2/F | DNA-directed RNA polymerase I subunit RPA4 |
 RPA14_YEAST

 2rf4 mmCIF Assemblies
 ---
 1| author_and_software_defined_assembly
 2| author_and_software_defined_assembly
 3| author_and_software_defined_assembly

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 41 residues in model #1.2 to IUPAC-
 IUB
 standards.
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 34,34,34, pixel
 0.766,0.761,0.727, shown at level 0.205, step 1, values float32

 > alphafold match #1

 Fetching AlphaFold database settings from
 https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json
 Fetching compressed AlphaFold P46669 from
 https://alphafold.ebi.ac.uk/files/AF-P46669-F1-model_v2.cif
 Fetching compressed AlphaFold P50106 from
 https://alphafold.ebi.ac.uk/files/AF-P50106-F1-model_v2.cif
 2 AlphaFold models found using UniProt identifiers: P46669 (chains
 A,A,C,C,E,E), P50106 (chains B,B,D,D,F,F)
 AlphaFold chains matching 2rf4
 ---
 Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
 B | RPA14_YEAST | P50106 | 1.71 | 52 | 61 | 100
 B | RPA14_YEAST | P50106 | 1.57 | 35 | 61 | 100
 D | RPA14_YEAST | P50106 | 1.59 | 52 | 60 | 100
 D F | RPA14_YEAST | P50106 | 1.65 | 35 | 60 | 100
 F | RPA14_YEAST | P50106 | 1.69 | 52 | 60 | 100
 A | RPA43_YEAST | P46669 | 1.66 | 171 | 174 | 100
 A | RPA43_YEAST | P46669 | 3.00 | 42 | 174 | 100
 C | RPA43_YEAST | P46669 | 1.48 | 171 | 172 | 100
 C | RPA43_YEAST | P46669 | 3.25 | 42 | 172 | 100
 E | RPA43_YEAST | P46669 | 1.58 | 171 | 175 | 100
 E | RPA43_YEAST | P46669 | 3.75 | 42 | 175 | 100

 Opened 12 AlphaFold models

 > show #2

 > select /A,B

 4213 atoms, 4302 bonds, 2 pseudobonds, 535 residues, 6 models selected

 > close #1.3#1-2#1.1-2

 Deleting Crystallographic maps (2rf4-sf.cif)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_sharp_32
 Deleting (LIVE) MDFF potential

 > open 3brw structureFactors true

 Summary of feedback from opening 3brw fetched from pdb
 ---
 warnings | Unknown polymer entity '5' near line 10839
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.
 notes | Fetching compressed mmCIF 3brw from
 http://files.rcsb.org/download/3brw.cif
 Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif
 Fetching compressed 3brw structure factors from
 http://files.rcsb.org/download/3brw-sf.cif
 Resolution: 3.400053747470817

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,28,22, pixel
 1.09,1.09,1.13,
 shown at level 0.155, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,28,22, pixel
 1.09,1.09,1.13,
 shown at level -0.0584,0.0584, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_40 as #1.1.1.4, grid size 38,28,22, pixel
 1.09,1.09,1.13, shown at level 0.332, step 1, values float32
 3brw title:
 Structure of the Rap-RapGAP complex [more info...]

 Chain information for 3brw
 ---
 Chain | Description | UniProt
 1.2/A 1.2/B 1.2/C | Rap1 GTPase-activating protein 1 | RPGP1_HUMAN
 1.2/D | Ras-related protein Rap-1b | RAP1B_HUMAN

 Non-standard residues in 3brw #1.2
 ---
 BEF — beryllium trifluoride ion
 MG — magnesium ion

 3brw mmCIF Assemblies
 ---
 1| author_defined_assembly
 2| author_defined_assembly
 3| author_defined_assembly
 4| author_defined_assembly

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 133 residues in model #1.2 to
 IUPAC-IUB
 standards.
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,28,22, pixel
 1.09,1.09,1.13, shown at level 0.152, step 1, values float32

 > alphafold match #1

 Fetching compressed AlphaFold P47736 from
 https://alphafold.ebi.ac.uk/files/AF-P47736-F1-model_v2.cif
 Fetching compressed AlphaFold P61224 from
 https://alphafold.ebi.ac.uk/files/AF-P61224-F1-model_v2.cif
 2 AlphaFold models found using UniProt identifiers: P47736 (chains A,B,C),
 P61224 (chain D)
 AlphaFold chains matching 3brw
 ---
 Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
 D | RAP1B_HUMAN | P61224 | 0.83 | 167 | 167 | 100
 A | RPGP1_HUMAN | P47736 | 1.85 | 341 | 336 | 99
 B | RPGP1_HUMAN | P47736 | 1.27 | 341 | 337 | 99
 C | RPGP1_HUMAN | P47736 | 1.80 | 341 | 332 | 99

 Opened 4 AlphaFold models

 > show #2

 > isolde restrain distances #1/A templateAtoms #2/A adjustForConfidence
 true
 > displayThreshold 0.5

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in
 model #2.1 to IUPAC-IUB standards.
 Fetching compressed Alphafold P47736 PAE from
 https://alphafold.ebi.ac.uk/files/AF-P47736-F1-predicted_aligned_error_v1.json
 RMSD between 330 pruned atom pairs is 1.430 angstroms; (across all 336
 pairs:
 1.835)
 RMSD between 5 pruned atom pairs is 2.688 angstroms; (across all 6 pairs:
 3.841)

 > isolde restrain distances #1/B templateAtoms #2/B adjustForConfidence
 true
 > displayThreshold 0.5

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in
 model #2.2 to IUPAC-IUB standards.
 RMSD between 334 pruned atom pairs is 1.071 angstroms; (across all 337
 pairs:
 1.249)

 > select #1/A,B

 5418 atoms, 5551 bonds, 676 residues, 1 model selected

 > hide #!2 models

 > select clear

 > show #!2 models

 > addh

 Summary of feedback from adding hydrogens to multiple structures
 ---
 warnings | Not adding hydrogens to 3brw #1.2/A THR 76 CB because it is
 missing
 heavy-atom bond partners
 Not adding hydrogens to 3brw #1.2/A LEU 411 CB because it is missing
 heavy-
 atom bond partners
 Not adding hydrogens to 3brw #1.2/B LYS 78 CB because it is missing heavy-
 atom
 bond partners
 Not adding hydrogens to 3brw #1.2/C LYS 78 CB because it is missing heavy-
 atom
 bond partners
 Not adding hydrogens to 3brw #1.2/C LEU 411 CB because it is missing
 heavy-
 atom bond partners
 notes | Termini for 3brw (#1.2) chain A determined from SEQRES records
 Termini for 3brw (#1.2) chain B determined from SEQRES records
 Termini for 3brw (#1.2) chain C determined from SEQRES records
 Termini for 3brw (#1.2) chain D determined from SEQRES records
 Chain-initial residues that are actual N termini: 3brw #1.2/D MET 1
 Chain-initial residues that are not actual N termini: 3brw #1.2/A THR 76,
 3brw
 #1.2/B LYS 78, 3brw #1.2/C LYS 78, 3brw #1.2/C PRO 330
 Chain-final residues that are actual C termini: 3brw #1.2/D ARG 167
 Chain-final residues that are not actual C termini: 3brw #1.2/A LEU 411,
 3brw
 #1.2/B ASP 414, 3brw #1.2/C GLY 325, 3brw #1.2/C GLY 413

 Traceback (most recent call last):
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\cmd_line\tool.py", line 302, in execute
 cmd.run(cmd_text)
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\core\commands\cli.py", line 2897, in run
 result = ci.function(session, **kw_args)
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\addh\cmd.py", line 62, in cmd_addh
 add_h_func(session, structures, template=template,
 in_isolation=in_isolation,
 **prot_schemes)
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\addh\cmd.py", line 161, in hbond_add_hydrogens
 hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\addh\cmd.py", line 168, in hbond_add_hydrogens
 _make_shared_data(session, structures, in_isolation)
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\addh\cmd.py", line 365, in _make_shared_data
 from chimerax.atom_search import AtomSearchTree
 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\atom_search\\__init__.py", line 15, in <module>
 import chimerax.atom_search_lib
 ModuleNotFoundError: No module named 'chimerax.atom_search_lib'

 ModuleNotFoundError: No module named 'chimerax.atom_search_lib'

 File "C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\chimerax\atom_search\\__init__.py", line 15, in
 import chimerax.atom_search_lib

 See log for complete Python traceback.


 > ui tool show Shell

 C:\Program Files\ChimeraX-daily\bin\lib\site-
 packages\jedi\inference\compiled\subprocess\functions.py:22: UserWarning:
 Module chimerax.atom_search.ast not importable in path
 ['C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\1.4\\\site-
 packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\python39.zip',
 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\DLLs', 'C:\\\Program
 Files\\\ChimeraX-daily\\\bin\\\lib', 'C:\\\Program Files\\\ChimeraX-
 daily\\\bin', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
 packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
 packages\\\win32', 'C:\\\Program Files\\\ChimeraX-
 daily\\\bin\\\lib\\\site-
 packages\\\win32\\\lib', 'C:\\\Program Files\\\ChimeraX-
 daily\\\bin\\\lib\\\site-packages\\\Pythonwin', '.', 'C:\\\Program
 Files\\\ChimeraX-daily\\\bin\\\lib\\\site-
 packages\\\IPython\\\extensions'].
 return access.load_module(inference_state, **kwargs)




 OpenGL version: 3.3.0 NVIDIA 497.29
 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation

 Locale: en_GB.cp1252
 Qt version: PyQt5 5.15.2, Qt 5.15.2
 Qt platform: windows

 Manufacturer: Notebook
 Model: P7xxTM1
 OS: Microsoft Windows 10 Education (Build 19041)
 Memory: 68,654,501,888
 MaxProcessMemory: 137,438,953,344
 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
 OSLanguage: en-GB

 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 3.0.0
     certifi: 2021.10.8
     cftime: 1.5.2
     charset-normalizer: 2.0.12
     ChimeraX-AddCharge: 1.2.3
     ChimeraX-AddH: 2.1.11
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2.1
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.3
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.36.2
     ChimeraX-AtomicLibrary: 6.1
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AxesPlanes: 2.1
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 2.0
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.6.1
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.2
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.2.2
     ChimeraX-Clipper: 0.18.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.5.1
     ChimeraX-CommandLine: 1.2.1
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.4.dev202203030220
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.2
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.5
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.1
     ChimeraX-Hbonds: 2.1.2
     ChimeraX-Help: 1.2
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.1
     ChimeraX-ImageFormats: 1.2
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.4.dev0
     ChimeraX-ItemsInspection: 1.0
     ChimeraX-Label: 1.1
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.5
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.1
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 2.0.6
     ChimeraX-MDcrds: 2.6
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.7
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.5.2
     ChimeraX-ModelPanel: 1.3.2
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0.2
     ChimeraX-OpenCommand: 1.8
     ChimeraX-PDB: 2.6.6
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.2
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0.1
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0.1
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.5
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.6
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.1
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.7.7
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-StructMeasure: 1.0.1
     ChimeraX-Struts: 1.0.1
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2.1
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.16.2
     ChimeraX-uniprot: 2.2
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.1.2
     ChimeraX-VIPERdb: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     comtypes: 1.1.10
     cxservices: 1.1
     cycler: 0.11.0
     Cython: 0.29.26
     debugpy: 1.5.1
     decorator: 5.1.1
     docutils: 0.17.1
     entrypoints: 0.4
     filelock: 3.4.2
     fonttools: 4.29.1
     funcparserlib: 1.0.0a0
     grako: 3.16.5
     h5py: 3.6.0
     html2text: 2020.1.16
     idna: 3.3
     ihm: 0.26
     imagecodecs: 2021.11.20
     imagesize: 1.3.0
     ipykernel: 6.6.1
     ipython: 7.31.1
     ipython-genutils: 0.2.0
     jedi: 0.18.1
     Jinja2: 3.0.3
     jupyter-client: 7.1.0
     jupyter-core: 4.9.2
     kiwisolver: 1.3.2
     line-profiler: 3.4.0
     lxml: 4.7.1
     lz4: 3.1.10
     MarkupSafe: 2.1.0
     matplotlib: 3.5.1
     matplotlib-inline: 0.1.3
     msgpack: 1.0.3
     nest-asyncio: 1.5.4
     netCDF4: 1.5.8
     networkx: 2.6.3
     numexpr: 2.8.1
     numpy: 1.22.1
     openvr: 1.16.802
     packaging: 21.3
     ParmEd: 3.4.3
     parso: 0.8.3
     pickleshare: 0.7.5
     Pillow: 9.0.0
     pip: 21.3.1
     pkginfo: 1.8.2
     prompt-toolkit: 3.0.28
     psutil: 5.9.0
     pycollada: 0.7.2
     pydicom: 2.2.2
     Pygments: 2.11.2
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 3.0.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.2
     pytz: 2021.3
     pywin32: 303
     pyzmq: 22.3.0
     qtconsole: 5.2.2
     QtPy: 2.0.1
     RandomWords: 0.3.0
     requests: 2.27.1
     scipy: 1.7.3
     setuptools: 59.8.0
     sfftk-rw: 0.7.1
     six: 1.16.0
     snowballstemmer: 2.2.0
     sortedcontainers: 2.4.0
     Sphinx: 4.3.2
     sphinx-autodoc-typehints: 1.15.2
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 3.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 2.0.0
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.5
     suds-community: 1.0.0
     tables: 3.7.0
     tifffile: 2021.11.2
     tinyarray: 1.2.4
     tornado: 6.1
     traitlets: 5.1.1
     urllib3: 1.26.8
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.37.1
     wheel-filename: 1.3.0
     WMI: 1.5.1

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6313>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → atom_search_lib missing

comment:3 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Yes, as you noted, fixed. It was broken for one day. There are other more obscure functions broken for the same reason that I will be fixing today. :-(

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